Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469. Determined by X-ray diffraction at 2.7 Å resolution. Released 22 Jan 2014.
Explore 4N7E in 3D Show helices and sheets RCSB PDB PDBe
4N7E contains 17 α-helices and 61 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 59-66 | 8 | |
| β-strand | 67-71 | 5 | 1 |
| β-strand | 78-84 | 7 | 2 |
| β-strand | 90-96 | 7 | 2 |
| β-strand | 109-114 | 6 | 2 |
| β-strand | 122-123 | 2 | 2 |
| α-helix | 125-128 | 4 | |
| β-strand | 133 | 1 | 3 |
| β-strand | 139-141 | 3 | 3 |
| α-helix | 142 | 1 | |
| β-strand | 149-153 | 5 | 3 |
| β-strand | 163-167 | 5 | 3 |
| β-strand | 175-178 | 4 | 3 |
| β-strand | 183 | 1 | 4 |
| β-strand | 188-189 | 2 | 5 |
| β-strand | 197-200 | 4 | 5 |
| β-strand | 201 | 1 | 4 |
| β-strand | 206-209 | 4 | 5 |
| β-strand | 217-220 | 4 | 5 |
| β-strand | 223-228 | 6 | 6 |
| β-strand | 234-238 | 5 | 6 |
| β-strand | 251-256 | 6 | 6 |
| β-strand | 264-276 | 13 | 6 |
| β-strand | 279-285 | 7 | 6 |
| β-strand | 292-297 | 6 | 6 |
| β-strand | 305-306 | 2 | 6 |
| α-helix | 307 | 1 | |
| β-strand | 312 | 1 | 6 |
| β-strand | 318-324 | 7 | 7 |
| β-strand | 327-333 | 7 | 7 |
| α-helix | 334 | 1 | |
| β-strand | 340-346 | 7 | 7 |
| β-strand | 353-361 | 9 | 7 |
| β-strand | 362 | 1 | 8 |
| β-strand | 369 | 1 | 8 |
| β-strand | 372-373 | 2 | 7 |
| β-strand | 381-386 | 6 | 7 |
| β-strand | 392-397 | 6 | 7 |
| β-strand | 404-405 | 2 | 7 |
| α-helix | 406 | 1 | |
| β-strand | 407-408 | 2 | 9 |
| α-helix | 409-410 | 2 | |
| β-strand | 426-429 | 4 | 9 |
| α-helix | 432-436 | 5 | |
| β-strand | 446 | 1 | 9 |
| β-strand | 455-462 | 8 | 9 |
| β-strand | 471-475 | 5 | 9 |
| β-strand | 483-486 | 4 | 9 |
| β-strand | 490-495 | 6 | 10 |
| α-helix | 496-498 | 3 | |
| β-strand | 500-505 | 6 | 10 |
| β-strand | 511 | 1 | 11 |
| β-strand | 513-517 | 5 | 10 |
| β-strand | 525-528 | 4 | 10 |
| β-strand | 534 | 1 | 11 |
| β-strand | 535-540 | 6 | 1 |
| β-strand | 549-555 | 7 | 1 |
| β-strand | 564-570 | 7 | 1 |
| β-strand | 578 | 1 | 12 |
| α-helix | 579 | 1 | |
| α-helix | 581-583 | 3 | |
| β-strand | 584-588 | 5 | 13 |
| β-strand | 602 | 1 | 13 |
| β-strand | 605-612 | 8 | 13 |
| β-strand | 619 | 1 | 12 |
| β-strand | 627-632 | 6 | 13 |
| α-helix | 633-635 | 3 | |
| α-helix | 637-639 | 3 | |
| β-strand | 640-642 | 3 | 14 |
| β-strand | 646-647 | 2 | 15 |
| β-strand | 656-657 | 2 | 15 |
| α-helix | 663-671 | 9 | |
| α-helix | 674-676 | 3 | |
| β-strand | 678-679 | 2 | 16 |
| β-strand | 682-684 | 3 | 14 |
| α-helix | 685 | 1 | |
| β-strand | 701-702 | 2 | 16 |
| α-helix | 704-708 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Sortilin | A | protein | 696 | Homo sapiens | Q99523 (AlphaFold model) |
>4N7E_1 Sortilin (chains A) SAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIM TFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRI FRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVC LAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASV MADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIF TSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRW THLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDA ISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCW QTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDY TIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDF GYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLK KKCTSNFLSPEKQNSKSNSGSAMIEGRGVGHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| 2JQ | 2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid | C15 H11 F3 N2 O3 | 1 |
Water and common crystallization additives (PGE) are not listed.
The identification of AF38469: An orally bioavailable inhibitor of the VPS10P family sorting receptor Sortilin. Schrder, T.J., Christensen, S., Lindberg, S. et al. Bioorg Med Chem Lett (2014) 24:177-180. DOI 10.1016/j.bmcl.2013.11.046 · PubMed
Other PDB entries of the same protein (UniProt Q99523 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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